Zavolan Lab

All

40 repositories

zarp
Public
The Zavolab Automated RNA-seq Pipeline
docker workflow bioinformatics rna-seq snakemake pipeline reproducible-research conda singularity fair
Python
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Apache License 2.0
•5•35•14•2•Updated Dec 22, 2024Dec 22, 2024
mirflowz
Public
Snakemake workflow for the mapping and quantification of miRNAs and isomiRs from miRNA-Seq libraries.
workflow bioinformatics snakemake mirna isomirs
Python
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MIT License
•1•6•26•2•Updated Dec 20, 2024Dec 20, 2024
IPA-immune
Public
Python
•
Apache License 2.0
•0•0•1•0•Updated Dec 11, 2024Dec 11, 2024
htsinfer
Public
Infer metadata for your downstream analysis straight from your RNA-Seq data
bioinformatics ngs inference high-throughput-sequencing hacktoberfest
Python
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Apache License 2.0
•23•11•6•0•Updated Nov 20, 2024Nov 20, 2024
zarp-cli
Public
A user-friendly command-line interface for the ZARP RNA-seq analysis workflow
python cli workflow library bioinformatics rna-seq snakemake pipeline reproducible-research sequencing
Python
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Apache License 2.0
•1•5•9•0•Updated Nov 1, 2024Nov 1, 2024
SCINPAS
Public
Single Cell Identification of Novel PolyA Sites.
Python
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Apache License 2.0
•0•3•4•0•Updated Sep 18, 2024Sep 18, 2024
polyAsite_Atlas_3
Public
The repository contains the data related to polyAsite Atlas v3 database and paper
HTML
•0•0•0•0•Updated Sep 11, 2024Sep 11, 2024
experimental-determination-elongation-rates
Public
Python
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MIT License
•0•0•0•0•Updated Aug 22, 2024Aug 22, 2024
mapping-translation-rates
Public
Python
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MIT License
•0•0•0•0•Updated Aug 22, 2024Aug 22, 2024
bCLIP_Stefanie_Jonas
Public
Jupyter Notebook
•0•0•0•0•Updated Jul 2, 2024Jul 2, 2024
logo
Public
Zavolab logo
Creative Commons Zero v1.0 Universal
•0•0•0•0•Updated Feb 3, 2024Feb 3, 2024
oligomap
Public
Oligomap is a program for fast identification of nearly-perfect matches of small RNAs in sequence databases.
Shell
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GNU General Public License v3.0
•0•0•0•0•Updated Nov 13, 2023Nov 13, 2023
scRNAsim-toolz
Public
A repository for the tools used by scRNAsim.
bioinformatics simulation scrna-seq
Python
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MIT License
•0•1•11•0•Updated Oct 27, 2023Oct 27, 2023
scRNAsim
Public
The projects implements a simulation of single cell RNA sequencing (scRNA-seq), accounting for some common sources noise that complicate the analysis of the resulting data.
Nextflow
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MIT License
•0•0•5•0•Updated Oct 23, 2023Oct 23, 2023
RCRUNCH
Public
Workflow for automated (e)CLIP analysis. From raw fastq to peak calling and motif analysis.
clip rna-binding-proteins bioinformatics
Python
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Apache License 2.0
•1•6•9•2•Updated Jan 24, 2023Jan 24, 2023
PAQR2
Public
Updated version of PAQR, which was previously available in the PAQR_KAPAC joint repository.
bioinformatics snakemake rna-seq-pipeline polyadenylation
Python
•
GNU General Public License v2.0
•0•7•4•1•Updated Dec 7, 2022Dec 7, 2022
Dockerfiles
Public
Dockerfile repository of the Zavolan Lab
Perl
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Apache License 2.0
•2•9•9•0•Updated Jul 8, 2022Jul 8, 2022
tandem-pas
Public
Extract set of tandem poly(A) sites from the PolyASite atlas.
bioinformatics snakemake polyadenylation
Perl
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Apache License 2.0
•0•2•2•0•Updated Feb 15, 2022Feb 15, 2022
bindz-rbp
Public
RBP module for bindz, a bioinformatics tool to detect regulators' binding sites on RNA sequences.
rna snakemake-workflows rna-binding-proteins bioinformatics-tool bioinformatics
Roff
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Apache License 2.0
•1•7•1•0•Updated Feb 14, 2022Feb 14, 2022
SCUREL
Public
Method to detect 3'UTR changes from scRNA-seq
scrnaseq snakemake-workflow bioinformatics
Python
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Apache License 2.0
•1•3•4•0•Updated Dec 16, 2021Dec 16, 2021
bindz-service
Public
Dockerfile
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Apache License 2.0
•0•1•0•0•Updated Nov 30, 2021Nov 30, 2021
PAQR_KAPAC
Public
scripts, pipelines and documentation to run PAQR and KAPAC; KAPAC allows to infer regulatory sequence motifs implicated in 3’ end processing changes; PAQR enables the quantification of poly(A) site usage from standard RNA-seq data
Python
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GNU General Public License v2.0
•4•8•9•0•Updated Nov 11, 2021Nov 11, 2021
tin-score-calculation
Public
Given a set of BAM files and a gene annotation BED file, calculates the Transcript Integrity Number (TIN) for each transcript.
bioinformatics quality-control rna-seq high-throughput-sequencing
Python
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GNU General Public License v3.0
•1•1•2•0•Updated Oct 29, 2021Oct 29, 2021
multiqc-plugins
Public
Custom plugins for the MultiQC tool.
bioinformatics high-throughput-sequencing bioinformatics-tool
HTML
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Apache License 2.0
•0•1•0•0•Updated Aug 24, 2021Aug 24, 2021
CFI2021
Public
Supplementary Materials
Jupyter Notebook
•0•0•0•0•Updated Jul 13, 2021Jul 13, 2021
zgtf
Public
gtf conversion utlity
genomics transcriptomics gtf-conversion-utlity
Python
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Apache License 2.0
•1•0•0•0•Updated Jun 17, 2021Jun 17, 2021
zpca
Public
PCA analysis
hacktoberfest
Python
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Apache License 2.0
•0•1•2•0•Updated Apr 9, 2021Apr 9, 2021
programming-for-life-sciences
Public archive
Toy repository for the Programming for Life Sciences course at the Biozentrum, University of Basel
teaching
Python
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Apache License 2.0
•3•4•0•0•Updated Oct 6, 2020Oct 6, 2020
merge_kallisto
Public
Merge kallisto results from multiple runs
R
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Apache License 2.0
•0•1•2•0•Updated Jun 18, 2020Jun 18, 2020
prune_tree
Public
Prune nh files based on a list of organisms
R
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Apache License 2.0
•0•0•0•0•Updated Jun 12, 2020Jun 12, 2020